AMBER Archive (2009)

Subject: RE: [AMBER] MD

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Jan 07 2009 - 18:33:46 CST

Dear John,

> What is the difference between an "equilibrium" and a "non-equilibrium"
> MD simulation?

To be honest I don't know the answer here, I don't know if I should know the
answer, or even if there is an answer...

I think that this question is potentially a very deep philosophical one. I
would actually go so far as to suggest that all of our simulations are
non-equilibrium since I doubt anybody can actually prove that a simulation
on nano to microsecond time scales is converged or equilibrated. In fact it
is probably hard to actually define what equilibrated is - especially if you
go to even longer time scales and you start to see large scale movements and
or rare events.

I guess the simple answer would be are the results such that the property
you are interested in converged, I.e. is its value no longer a function of
the initial conditions? This would be an equilibrium MD simulation, you
would of course have to go through initial non-equilibrium dynamics to get
there.

Alternatively one could probably call a non-equilibrium MD simulation the
part of your simulation where you want to observe how something relaxes from
a perturbed state - for example you deliberately start from a strained
conformation and watch how it changes or perhaps you do something like
jarzinski pulling where you run a large number of targeted MD runs and then
essentially combine them to give you an average property.

In essence though I don't think there is an exact definition one could use
and indeed whether the separation of "equilibrium" of "non-equilibrium" MD
simulation can be made. At least it isn't in, my experience, a generally
accepted term.

Perhaps others can comment more...

All the best
Ross

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|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
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